null Sun 23 Dec 23:46:37 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gvh-2.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-2.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-2.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 23:46:42 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 856 and 0 Target number of residues in the AU: 856 Target solvent content: 0.6147 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-2.6-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-2.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 121.211 2.600 Wilson plot Bfac: 58.86 32893 reflections ( 89.68 % complete ) and 0 restraints for refining 7731 atoms. Observations/parameters ratio is 1.06 ------------------------------------------------------ Starting model: R = 0.3537 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2732 (Rfree = 0.000) for 7731 atoms. Found 78 (125 requested) and removed 121 (62 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.88 2.48 NCS extension: 0 residues added, 7688 seeds are put forward Round 1: 487 peptides, 74 chains. Longest chain 16 peptides. Score 0.451 Round 2: 524 peptides, 63 chains. Longest chain 29 peptides. Score 0.554 Round 3: 563 peptides, 62 chains. Longest chain 29 peptides. Score 0.600 Round 4: 558 peptides, 58 chains. Longest chain 29 peptides. Score 0.614 Round 5: 580 peptides, 57 chains. Longest chain 50 peptides. Score 0.640 Taking the results from Round 5 Chains 61, Residues 523, Estimated correctness of the model 74.8 % 6 chains (70 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 13199 restraints for refining 6440 atoms. 10903 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3135 (Rfree = 0.000) for 6440 atoms. Found 104 (104 requested) and removed 90 (52 requested) atoms. Cycle 2: After refmac, R = 0.2930 (Rfree = 0.000) for 6402 atoms. Found 58 (104 requested) and removed 73 (52 requested) atoms. Cycle 3: After refmac, R = 0.2824 (Rfree = 0.000) for 6362 atoms. Found 64 (103 requested) and removed 59 (51 requested) atoms. Cycle 4: After refmac, R = 0.2682 (Rfree = 0.000) for 6354 atoms. Found 52 (103 requested) and removed 62 (51 requested) atoms. Cycle 5: After refmac, R = 0.2632 (Rfree = 0.000) for 6327 atoms. Found 52 (102 requested) and removed 55 (51 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.94 2.53 NCS extension: 83 residues added (38 deleted due to clashes), 6455 seeds are put forward Round 1: 554 peptides, 56 chains. Longest chain 33 peptides. Score 0.619 Round 2: 580 peptides, 55 chains. Longest chain 31 peptides. Score 0.648 Round 3: 576 peptides, 54 chains. Longest chain 38 peptides. Score 0.649 Round 4: 590 peptides, 55 chains. Longest chain 35 peptides. Score 0.658 Round 5: 586 peptides, 51 chains. Longest chain 32 peptides. Score 0.671 Taking the results from Round 5 Chains 62, Residues 535, Estimated correctness of the model 78.6 % 13 chains (200 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 11467 restraints for refining 6443 atoms. 8606 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2831 (Rfree = 0.000) for 6443 atoms. Found 88 (104 requested) and removed 80 (52 requested) atoms. Cycle 7: After refmac, R = 0.2642 (Rfree = 0.000) for 6415 atoms. Found 72 (104 requested) and removed 65 (52 requested) atoms. Cycle 8: After refmac, R = 0.2537 (Rfree = 0.000) for 6397 atoms. Found 65 (104 requested) and removed 66 (52 requested) atoms. Cycle 9: After refmac, R = 0.2417 (Rfree = 0.000) for 6369 atoms. Found 48 (103 requested) and removed 54 (51 requested) atoms. Cycle 10: After refmac, R = 0.2381 (Rfree = 0.000) for 6347 atoms. Found 46 (103 requested) and removed 56 (51 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.97 2.56 NCS extension: 76 residues added (31 deleted due to clashes), 6440 seeds are put forward Round 1: 550 peptides, 50 chains. Longest chain 36 peptides. Score 0.643 Round 2: 576 peptides, 51 chains. Longest chain 35 peptides. Score 0.662 Round 3: 613 peptides, 45 chains. Longest chain 63 peptides. Score 0.717 Round 4: 598 peptides, 46 chains. Longest chain 49 peptides. Score 0.702 Round 5: 575 peptides, 42 chains. Longest chain 40 peptides. Score 0.699 Taking the results from Round 3 Chains 51, Residues 568, Estimated correctness of the model 83.8 % 17 chains (311 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 246 C and 256 C 48 chains (571 residues) following loop building 16 chains (320 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 10267 restraints for refining 6443 atoms. 6816 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2662 (Rfree = 0.000) for 6443 atoms. Found 90 (104 requested) and removed 75 (52 requested) atoms. Cycle 12: After refmac, R = 0.2528 (Rfree = 0.000) for 6417 atoms. Found 79 (102 requested) and removed 66 (52 requested) atoms. Cycle 13: After refmac, R = 0.2326 (Rfree = 0.000) for 6415 atoms. Found 41 (100 requested) and removed 58 (52 requested) atoms. Cycle 14: After refmac, R = 0.2249 (Rfree = 0.000) for 6385 atoms. Found 42 (97 requested) and removed 51 (51 requested) atoms. Cycle 15: After refmac, R = 0.2197 (Rfree = 0.000) for 6365 atoms. Found 36 (95 requested) and removed 51 (51 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.96 2.55 NCS extension: 364 residues added (137 deleted due to clashes), 6740 seeds are put forward Round 1: 576 peptides, 48 chains. Longest chain 41 peptides. Score 0.675 Round 2: 620 peptides, 38 chains. Longest chain 59 peptides. Score 0.749 Round 3: 620 peptides, 47 chains. Longest chain 44 peptides. Score 0.715 Round 4: 618 peptides, 42 chains. Longest chain 51 peptides. Score 0.733 Round 5: 622 peptides, 51 chains. Longest chain 58 peptides. Score 0.701 Taking the results from Round 2 Chains 48, Residues 582, Estimated correctness of the model 87.0 % 15 chains (327 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 A and 120 A 45 chains (585 residues) following loop building 14 chains (335 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 9939 restraints for refining 6444 atoms. 6357 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2519 (Rfree = 0.000) for 6444 atoms. Found 83 (94 requested) and removed 69 (52 requested) atoms. Cycle 17: After refmac, R = 0.2313 (Rfree = 0.000) for 6415 atoms. Found 72 (92 requested) and removed 61 (52 requested) atoms. Cycle 18: After refmac, R = 0.2243 (Rfree = 0.000) for 6410 atoms. Found 46 (89 requested) and removed 54 (52 requested) atoms. Cycle 19: After refmac, R = 0.2163 (Rfree = 0.000) for 6388 atoms. Found 47 (87 requested) and removed 51 (51 requested) atoms. Cycle 20: After refmac, R = 0.2135 (Rfree = 0.000) for 6371 atoms. Found 69 (84 requested) and removed 52 (51 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 2.58 NCS extension: 213 residues added (177 deleted due to clashes), 6620 seeds are put forward Round 1: 590 peptides, 39 chains. Longest chain 51 peptides. Score 0.723 Round 2: 632 peptides, 40 chains. Longest chain 51 peptides. Score 0.750 Round 3: 648 peptides, 44 chains. Longest chain 60 peptides. Score 0.747 Round 4: 632 peptides, 42 chains. Longest chain 66 peptides. Score 0.743 Round 5: 637 peptides, 40 chains. Longest chain 76 peptides. Score 0.753 Taking the results from Round 5 Chains 49, Residues 597, Estimated correctness of the model 87.3 % 15 chains (373 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 A and 89 A Built loop between residues 115 A and 119 A Built loop between residues 64 C and 70 C Built loop between residues 118 C and 122 C Built loop between residues 248 C and 252 C Built loop between residues 81 B and 86 B 37 chains (606 residues) following loop building 9 chains (395 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 9356 restraints for refining 6444 atoms. 5504 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2663 (Rfree = 0.000) for 6444 atoms. Found 83 (83 requested) and removed 70 (52 requested) atoms. Cycle 22: After refmac, R = 0.2379 (Rfree = 0.000) for 6428 atoms. Found 81 (81 requested) and removed 65 (52 requested) atoms. Cycle 23: After refmac, R = 0.2229 (Rfree = 0.000) for 6432 atoms. Found 71 (79 requested) and removed 55 (52 requested) atoms. Cycle 24: After refmac, R = 0.2171 (Rfree = 0.000) for 6437 atoms. Found 51 (77 requested) and removed 58 (52 requested) atoms. Cycle 25: After refmac, R = 0.2174 (Rfree = 0.000) for 6422 atoms. Found 62 (75 requested) and removed 53 (52 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 2.58 NCS extension: 234 residues added (212 deleted due to clashes), 6711 seeds are put forward Round 1: 615 peptides, 43 chains. Longest chain 61 peptides. Score 0.727 Round 2: 636 peptides, 41 chains. Longest chain 72 peptides. Score 0.749 Round 3: 616 peptides, 40 chains. Longest chain 75 peptides. Score 0.739 Round 4: 621 peptides, 37 chains. Longest chain 62 peptides. Score 0.753 Round 5: 634 peptides, 39 chains. Longest chain 72 peptides. Score 0.755 Taking the results from Round 5 Chains 46, Residues 595, Estimated correctness of the model 87.5 % 18 chains (417 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 246 A and 253 A Built loop between residues 115 C and 120 C Built loop between residues 171 C and 176 C Built loop between residues 246 C and 252 C Built loop between residues 115 B and 119 B Built loop between residues 236 B and 241 B 38 chains (616 residues) following loop building 12 chains (443 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 9072 restraints for refining 6444 atoms. 5013 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2621 (Rfree = 0.000) for 6444 atoms. Found 73 (73 requested) and removed 75 (52 requested) atoms. Cycle 27: After refmac, R = 0.2453 (Rfree = 0.000) for 6411 atoms. Found 71 (71 requested) and removed 68 (52 requested) atoms. Cycle 28: After refmac, R = 0.2327 (Rfree = 0.000) for 6395 atoms. Found 60 (69 requested) and removed 54 (52 requested) atoms. Cycle 29: After refmac, R = 0.2285 (Rfree = 0.000) for 6390 atoms. Found 54 (66 requested) and removed 54 (51 requested) atoms. Cycle 30: After refmac, R = 0.2243 (Rfree = 0.000) for 6380 atoms. Found 50 (64 requested) and removed 53 (51 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.58 NCS extension: 372 residues added (187 deleted due to clashes), 6777 seeds are put forward Round 1: 610 peptides, 47 chains. Longest chain 54 peptides. Score 0.707 Round 2: 628 peptides, 42 chains. Longest chain 60 peptides. Score 0.740 Round 3: 618 peptides, 40 chains. Longest chain 55 peptides. Score 0.740 Round 4: 627 peptides, 39 chains. Longest chain 82 peptides. Score 0.750 Round 5: 621 peptides, 41 chains. Longest chain 51 peptides. Score 0.738 Taking the results from Round 4 Chains 46, Residues 588, Estimated correctness of the model 87.1 % 15 chains (396 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 65 A Built loop between residues 85 A and 89 A Built loop between residues 115 A and 121 A Built loop between residues 194 C and 197 C Built loop between residues 230 B and 238 B 38 chains (604 residues) following loop building 10 chains (415 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 9505 restraints for refining 6443 atoms. 5532 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2565 (Rfree = 0.000) for 6443 atoms. Found 62 (62 requested) and removed 79 (52 requested) atoms. Cycle 32: After refmac, R = 0.2333 (Rfree = 0.000) for 6402 atoms. Found 60 (60 requested) and removed 63 (52 requested) atoms. Cycle 33: After refmac, R = 0.2232 (Rfree = 0.000) for 6381 atoms. Found 54 (58 requested) and removed 54 (51 requested) atoms. Cycle 34: After refmac, R = 0.2217 (Rfree = 0.000) for 6372 atoms. Found 55 (56 requested) and removed 52 (51 requested) atoms. Cycle 35: After refmac, R = 0.2190 (Rfree = 0.000) for 6371 atoms. Found 48 (54 requested) and removed 53 (51 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.99 2.58 NCS extension: 290 residues added (181 deleted due to clashes), 6667 seeds are put forward Round 1: 621 peptides, 42 chains. Longest chain 69 peptides. Score 0.735 Round 2: 650 peptides, 39 chains. Longest chain 66 peptides. Score 0.766 Round 3: 636 peptides, 40 chains. Longest chain 56 peptides. Score 0.753 Round 4: 645 peptides, 36 chains. Longest chain 71 peptides. Score 0.772 Round 5: 632 peptides, 41 chains. Longest chain 63 peptides. Score 0.746 Taking the results from Round 4 Chains 43, Residues 609, Estimated correctness of the model 89.1 % 17 chains (450 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 A and 103 A Built loop between residues 190 A and 198 A Built loop between residues 37 C and 47 C Built loop between residues 68 C and 71 C Built loop between residues 83 C and 89 C Built loop between residues 115 C and 119 C Built loop between residues 135 C and 140 C Built loop between residues 246 C and 251 C Built loop between residues 81 B and 89 B Built loop between residues 231 B and 235 B 29 chains (644 residues) following loop building 7 chains (496 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 8619 restraints for refining 6444 atoms. 4142 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2565 (Rfree = 0.000) for 6444 atoms. Found 52 (52 requested) and removed 77 (52 requested) atoms. Cycle 37: After refmac, R = 0.2321 (Rfree = 0.000) for 6397 atoms. Found 52 (52 requested) and removed 67 (52 requested) atoms. Cycle 38: After refmac, R = 0.2190 (Rfree = 0.000) for 6368 atoms. Found 50 (51 requested) and removed 58 (51 requested) atoms. Cycle 39: After refmac, R = 0.2151 (Rfree = 0.000) for 6351 atoms. Found 49 (51 requested) and removed 52 (51 requested) atoms. Cycle 40: After refmac, R = 0.2134 (Rfree = 0.000) for 6341 atoms. Found 34 (51 requested) and removed 53 (51 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.00 2.58 NCS extension: 448 residues added (198 deleted due to clashes), 6793 seeds are put forward Round 1: 619 peptides, 37 chains. Longest chain 87 peptides. Score 0.752 Round 2: 621 peptides, 38 chains. Longest chain 71 peptides. Score 0.749 Round 3: 633 peptides, 33 chains. Longest chain 83 peptides. Score 0.775 Round 4: 623 peptides, 32 chains. Longest chain 77 peptides. Score 0.772 Round 5: 620 peptides, 38 chains. Longest chain 73 peptides. Score 0.749 Taking the results from Round 3 Chains 35, Residues 600, Estimated correctness of the model 89.3 % 11 chains (377 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 244 A and 248 A Built loop between residues 87 C and 91 C Built loop between residues 115 C and 118 C Built loop between residues 116 B and 120 B 30 chains (610 residues) following loop building 7 chains (388 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 9805 restraints for refining 6443 atoms. 5914 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2538 (Rfree = 0.000) for 6443 atoms. Found 52 (52 requested) and removed 70 (52 requested) atoms. Cycle 42: After refmac, R = 0.2372 (Rfree = 0.000) for 6407 atoms. Found 52 (52 requested) and removed 67 (52 requested) atoms. Cycle 43: After refmac, R = 0.2251 (Rfree = 0.000) for 6375 atoms. Found 51 (51 requested) and removed 56 (51 requested) atoms. Cycle 44: After refmac, R = 0.2174 (Rfree = 0.000) for 6362 atoms. Found 51 (51 requested) and removed 53 (51 requested) atoms. Cycle 45: After refmac, R = 0.2127 (Rfree = 0.000) for 6348 atoms. Found 44 (51 requested) and removed 53 (51 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.01 2.59 NCS extension: 122 residues added (177 deleted due to clashes), 6474 seeds are put forward Round 1: 609 peptides, 43 chains. Longest chain 58 peptides. Score 0.722 Round 2: 644 peptides, 39 chains. Longest chain 78 peptides. Score 0.762 Round 3: 655 peptides, 35 chains. Longest chain 85 peptides. Score 0.782 Round 4: 642 peptides, 41 chains. Longest chain 83 peptides. Score 0.753 Round 5: 631 peptides, 41 chains. Longest chain 50 peptides. Score 0.746 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 620, Estimated correctness of the model 89.9 % 16 chains (469 residues) have been docked in sequence Sequence coverage is 75 % Consider running further cycles of model building using 2gvh-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 84 A and 90 A Built loop between residues 234 A and 239 A Built loop between residues 217 C and 220 C Built loop between residues 87 B and 91 B Built loop between residues 115 B and 118 B Built loop between residues 172 B and 176 B Built loop between residues 191 B and 194 B Built loop between residues 243 B and 252 B 33 chains (639 residues) following loop building 8 chains (498 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 32893 reflections ( 89.68 % complete ) and 8634 restraints for refining 6444 atoms. 4172 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2456 (Rfree = 0.000) for 6444 atoms. Found 0 (52 requested) and removed 52 (52 requested) atoms. Cycle 47: After refmac, R = 0.2279 (Rfree = 0.000) for 6358 atoms. Found 0 (51 requested) and removed 18 (51 requested) atoms. Cycle 48: After refmac, R = 0.2181 (Rfree = 0.000) for 6328 atoms. Found 0 (51 requested) and removed 16 (51 requested) atoms. Cycle 49: After refmac, R = 0.2072 (Rfree = 0.000) for 6303 atoms. Found 0 (51 requested) and removed 11 (51 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:09:09 GMT 2018 Job finished. TimeTaking 82.53 Used memory is bytes: 24049256